Mercurial > repos > biomonika > test_dependency
changeset 19:535f23f73595
d11
| author | biomonika <biomonika@psu.edu> |
|---|---|
| date | Mon, 25 Aug 2014 15:28:15 -0400 |
| parents | c0eaad1712e0 |
| children | 479f6826477b |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 26 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- a/tool_dependencies.xml Mon Aug 25 15:19:09 2014 -0400 +++ b/tool_dependencies.xml Mon Aug 25 15:28:15 2014 -0400 @@ -17,4 +17,30 @@ </install> <readme>Compiling samtools with fPIC in order to create bam.h and compiled libbam.a files</readme> </package> + + <package name="perl" version="5.18.1"> + <repository name="package_perl_5_18" owner="iuc" prior_installation_required="True" /> + </package> + + <package name="bioperl" version="1.6.922"> + <install version="1.0"> + <actions> + <action type="setup_perl_environment"> + <repository changeset_revision="28865aa39fbb" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="perl" version="5.18.1" /> + </repository> + <!-- allow downloading and installing an Perl package from cpan.org--> + <package>Bio::DB::Sam</package> + <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-SamTools-1.39.tar.gz</package> + <package>Bio::DB::Fasta</package> + <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz</package> + <package>File::Slurp</package> + <package>http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/File-Slurp-9999.13.tar.gz</package> + </action> + </actions> + </install> + <readme> + Installing dependencies. Bio::DB::Sam needs to know location of bam.h and compiled libbam.a files, therefore environmental variable SAMTOOLS needs to be correctly set. + </readme> + </package> </tool_dependency> \ No newline at end of file